A protein motif, sometimes referred to as a supersecondary structure, is the term used to describe certain common combinations of secondary structure elements that are observed frequently in protein structures. Protein motifs provide a useful way of categorizing distinctive and recurring components of protein structure. In the hierarchy of protein structure classification, the protein motif falls between that of secondary structure and tertiary structure. Classification of these preferred patterns of packing secondary structure elements is somewhat arbitrary, and there is sometimes overlap between the structural terms of protein motifs and protein domains. However, unlike domains, protein motifs do not necessarily fold independently of the rest of the polypeptide chain, and they may not always have an intrinsic function.
Proteins having structurally similar motifs can share significant sequence identity in the equivalent regions of the polypeptide chain, even if there is very low sequence identity overall. The identification of regions of conserved sequence within proteins means that novel protein motifs can be predicted using sequence information only, in the absence of any three-dimensional structural data. The Kringle domain is an example of such a sequence motif, in that it is easily identified from protein sequences based on three characteristic disulfide bonds. Other protein motifs are purely structural and have little or no sequence conservation; examples include the b-meander, the Greek key, and the jelly roll.
